สถาบันวิจัยวิทยาศาสตร์สาธารณสุข

NATIONAL INSTITUTE OF HEALTH OF THAILAND

Nomenclature Variation as a Component in Assessing the Consistency of Identification of Pseudomonads and Related Organisms

Authors : Micah I. Krichevsky*, Paul De Vos**,Mark Segal***,Elaine J. Krichevsky*Surang Dejsirilert****, Patrick Gillevet*****,Deborah Henry******, Jorge Lalucat*******, Edward Moore********,Jane Tang*********,Sue Whitehead**********, Yuguang Zhou ***********, Hans Yu************

Affiliations:        *Bionomics International, USA

**University of Gent, Belgium
***Environmental Protection Agency, USA
****National Institute of Health, Thailand
*****George Mason University, USA
******University of British Columbia, Research Centre, Canada
*******Universitat de les Illes Balears, Spain
******** The Macaulay Research Institute, Scotland, U.K
*********American Type Culture Collection, USA
**********British Colombia Institute of Technology, Canada
***********CAS, China General Microbiological Culture Collection Center, Institute of Microbiolgy, China
************Health Canada, Canada
 
Source:             Joint Statistical Meetings, Minneapolis, MN, USA, 10 August 2005
 
Language:         English
 
Abstract:
 
Background: Those wanting identification of unknown bacteria need to know the reproducibility of identifications, especially to determine possible pathogenicity and to support regulatory assessments of potential hazard. Sponsored by Health Canada, 300 isolates (Phase I, 2000-2003) of PseudomonasBurkholderia and related genera were sent to 8 laboratories for identification. (Phase II is ongoing, 2003-2006.) The aim is to evaluate reproducibility. The laboratories varied in mission and methodologies. A serious issue in identification is the underlying nomenclatures used by taxonomists, commercial or personal identification methods, public data banks, etc. We wished to separate the inconsistencies in identification due to nomenclature from variations in the laboratory data.
 
Methods: A distributing laboratory sent randomly encoded cultures to each laboratory. Using their own methods, each laboratory submitted best estimates of the isolates’ identities with supporting data. We created databases of genera, species, subspecific identifications, identificationfailures and primary data. To normalize the taxon names we used the name reported by the contributor of the initial cultureand the name in the Approved Lists of Bacterial Names for each Phase. We tabulated the consistency of identification across laboratories using the original names assigned and adjusted according to the official names for each of the dates certain.
 
Results: We report: 1) The species names originally submitted for the study; 2) The species identifications originally given by the laboratories; 3) The species names changed as of Phase I; 4) The species names changed as of Phase II; 5) The invalid Phase I or Phase II names submitted by the laboratories i.e., not in the April, 2000 or April, 2003 Approved List, respectively; and 7) The names from GENBANK/EMBL vs. RDB for individual 16s RNA sequences.
 
Conclusions: The information illustrates the profound lag in transfer to and use of nomenclatural information by the practitioners of the art of identification. The consistency of identification improved when reported names were adjusted for name changes to a date certain. The adjustments allowed differentiation of the analytical capabilities of labs and methods, unfettered by naming discrepancies.